There is a Bentley Manual for your car (http://www.bentleypublishers.com/bm...5-series-e60-e61-repair-manual-2004-2010.html) - If you're ambitious, have tools, workspace, time, and are mechanically inclined, there's probably no reason to think that, with the guidance of the manual's instructions, you might not be able to tackle the project. My familiarity is with the much older cars, where this type of task, although not the simplest, is still relatively straightforward - I would expect the job for your car to be a more complicated and time consuming, one reason likely being that a lot more needs to be disassembled and removed just to gain access to begin the r&r (removal/replacement) of the water pump.

Bavarian Autosport (Bavauto.com) lists a water pump for a 2006 550i $252.95, with belt, gasket, & o-ring an additional $46 (note that I have no idea if that's all the parts that may be necessary - perhaps it's appropriate to do a thermostat, or hoses, or other things as well) - In any case, it would appear you're looking at parts being a bit more than $300 minimum, depending on how you source them and what all else you may need, not including coolant, and it may be recommended to use BMW's coolant.

I would guess that would be at least a 4-hr. job for any dealer/shop (minimum, maybe it takes a day, and I might not be surprised if it took longer), so, looking at dealer rates, guessing, of $110-$130/hr, plus shop materials and waste processing disposal fees, so perhaps the labor/etc. r&r charge maybe runs up to $600 (if it's a 4-hr. job) - and, don't forget sales tax. Of course there's shipping/handling for parts you might buy. I think most shops may refuse to install customer-supplied parts for a whole host of reason, so if you're hoping to shop your own parts and ask somebody else to install them, you may want to check that before buying any parts.

A phone call to any shop or dealer, and they should be able to give you an accurate estimate of what they have to charge for the job.